The GTPase Activating Rap/RanGAP Domain-Like 1 Gene Is Associated with Chicken Reproductive Traits

Abstract

BackgroundAbundant evidence indicates that chicken reproduction is strictly regulated by the hypothalamic-pituitary-gonad (HPG) axis, and the genes included in the HPG axis have been studied extensively. However, the question remains as to whether any other genes outside of the HPG system are involved in regulating chicken reproduction. The present study was aimed to identify, on a genome-wide level, novel genes associated with chicken reproductive traits.Methodology/Principal FindingSuppressive subtractive hybridization (SSH), genome-wide association study (GWAS), and gene-centric GWAS were used to identify novel genes underlying chicken reproduction. Single marker-trait association analysis with a large population and allelic frequency spectrum analysis were used to confirm the effects of candidate genes. Using two full-sib Ningdu Sanhuang (NDH) chickens, GARNL1 was identified as a candidate gene involved in chicken broodiness by SSH analysis. Its expression levels in the hypothalamus and pituitary were significantly higher in brooding chickens than in non-brooding chickens. GWAS analysis with a NDH two tail sample showed that 2802 SNPs were significantly associated with egg number at 300 d of age (EN300). Among the 2802 SNPs, 2 SNPs composed a block overlapping the GARNL1 gene. The gene-centric GWAS analysis with another two tail sample of NDH showed that GARNL1 was strongly associated with EN300 and age at first egg (AFE). Single marker-trait association analysis in 1301 female NDH chickens confirmed that variation in this gene was related to EN300 and AFE. The allelic frequency spectrum of the SNP rs15700989 among 5 different populations supported the above associations. Western blotting, RT-PCR, and qPCR were used to analyze alternative splicing of the GARNL1 gene. RT-PCR detected 5 transcripts and revealed that the transcript, which has a 141 bp insertion, was expressed in a tissue-specific manner.Conclusions/SignificanceOur findings demonstrate that the GARNL1 gene contributes to chicken reproductive traits.

Genome-wide association study of 8 carcass traits in Jinghai Yellow chickens using specific-locus amplified fragment sequencing technology

“…GWAS are commonly used to identify SNP associated with economically important production traits in animal studies (Jiang et al., 2010 ; Fan et al., 2011 ; Shen et al., 2012 ). SLAF-seq technology is a cost-effective way to genotype SNP in such analyses, because it can develop many specific markers and achieve a high success rate (Sun et al., 2013 ).…”

Population Genomic Analyses Based on 1 Million SNPs in Commercial Egg Layers

“…Specifically, brown layers were bred for meat production as well as egg-production, whereas white egg layers were bred only for egg production [5]. SREBF2 and RALGAPA1 , which are both associated with reproductive traits and broodiness [41], [42], were also located in the regions with high contrast between the two layer breeds. This can indicate that different regions were selected for reproductive traits in the different egg-layer breeds.…”

Genome-Wide Association Analysis Reveals Key Genes Responsible for Egg Production of Lion Head Goose

“…Hoglund et al found that a total of 17,388 significant SNP markers and candidate genes associated with female fertility were distributed on 25 chromosomes in the Nordic Red cattle group (Hoglund et al, 2015). Shen et al carried out GWAS on Ningdu Sanhuang chickens with Chicken chip and found the candidate gene, GARNL1, which was related to reproductive traits (Shen et al, 2012). Xie used the Illumina Porcine SNP60K chip to screen the potential candidate genes that may be associated with the litter size of the Xiang Pig (Xie, 2016).…”